title: Hs_Cyt49_PancreasD10_0.1%Digitonin_ATAC-seq_E

description: ATAC-seq of PP cells-replicate 2

data_processing:
adaptors were trimmed from ATAC-Seq reads using the trim_galore package
reads were mapped to human reference genome hg19 using bwa
mapeped reads were filtered by Samtools, skip alignment with MAPQ smaller than 30, remove duplicate reads, remove mitochondrial reads
peaks were called using mac2, with the parameters: --nomodel --shift -100 --extsize 200 -B --broad --keep-dup all --nolambda
Genome_build: hg19
Supplementary_files_format_and_content: peak file in bed format

extract_protocol:
Genomic DNA was extracted using Dneasy Blood and Tissue Kit from Qiagen.
Libraries were prepared using the protocol from Dr. Christopher Glass's lab. Briefly, pancreatic progenitors are collected and lysed using spin lysis buffer mix. Next, transposition reaction was performed using reaction mix and then DNA was purified using Zymo DNA clean and concentrator. Lastly, DNA product was amplified by PCR and then gel purified for tapestation analysis.

treatment_protocol: Pancreatic progenitor stage cells were collected and then genomic DNA was extracted to proceeded to ATAC-seq library preparation.


title: Hs_H1_WT_D8-10-miR-375_RNAseq_2

status: Public on Nov 14 2019

type: SRA

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

country: USA

institute: UC San Diego

description:
RNA-seq of PP cells transduced with miR-375 at day8 and harvested at day10-replicate2.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt

library_source: transcriptomic

data_processing:
Reads were aligned to the hg19 by STAR with parameters: --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --runThreadN 5. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflink.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: PE_day10_rpkm_values.txt: Gene expression (RPKM) data table in tab-delimited text format.

molecule: total RNA

organism: Homo sapiens

source_name: Pancreatic progenitor cells

growth_protocol: Pancreatic progenitor stage cells were cultured in stage 4 medium (MCDB 131 medium, 2.5 g/L NaHCO3, 1X GlutaMAX, 10 mM D-glucose, 2% BSA) and supplemented with 0.25 mM L-Ascorbic Acid (VIT-C), 2 ng/mL FGF7, 0.25 µM SANT-1, 0.1 µM Retinoic Acid, 200 nM LDN193189, 1:200 ITS-X, 100nM TPB and incubated at 37˚C and 5% CO2.

extract_protocol:
mRNA was extracted using miRNeasy mini kit from Qiagen.
Libraries were prepared using the protocol from Dr. Sander lab. Briefly, RNA were first poly A selected and then subject to RNA fragmentation. Then fragmented RNA were proceeded with first stand synthesis, second strand synthesis, end repair and A-tailing. Resulting product was ligated with adaptor and selected by size, and next were enriched using PCR. At last DNA purification was performed and samples sent out for sequencing.

treatment_protocol: Pancreatic progenitor stage cells were collected and then mRNA was extracted to proceeded to RNA-seq library preparation.

tag: cell type

value: ES-derived pancreatic progenitor cells

tag: es cell line

tag: transduction

value: miR-375 at day8


title: hu_Cyt49_PancreasD10_ATAC-seq_A

description:
ATAC-seq of PP cells-replicate 1.
Endocrine tissue

library_source: genomic

data_processing:
Adaptors were trimmed from ATAC-Seq reads using the trim_galore package.
Reads were mapped to human reference genome hg19 using bwa.
Mapped reads were filtered by Samtools, skip alignment with MAPQ smaller than 30, remove duplicate reads, remove mitochondrial reads.
Peaks were called using mac2, with the parameters: --nomodel --shift -100 --extsize 200 -B --broad --keep-dup all --nolambda
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: huCyt49_PancreasD10_ATAC_seq_A_S15_L008.rmdup.nolambda.bed: Peak file in bed format.

molecule: genomic DNA

extract_protocol:
Genomic DNA was extracted using DNeasy Blood and Tissue Kit from Qiagen.
Libraries were prepared using the protocol from Dr. Christopher Glass's lab. Briefly, pancreatic progenitors were collected and lysed using spin lysis buffer mix. Next, transposition reaction was performed using reaction mix and then DNA was purified using Zymo DNA clean and concentrator. Lastly, DNA product was amplified by PCR and then gel purified for TapeStation analysis.


title: Hs_H1_WT_D8-10-miR-200a_RNAseq_2

description:
RNA-seq of PP cells transduced with miR-200a at day8 and harvested at day10-replicate2.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt

value: miR-200a at day8


title: Hs_H1_WT_D8-10-EV_RNAseq_3

description:
RNA-seq of PP cells transduced with empty vector control at day8 and harvested at day10-replicate3.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt

value: empty vector control at day8


title: Hs_H1_WT_D8-10-miR-poly_RNAseq_2

description:
RNA-seq of PP cells transduced with Poly-miR at day8 and harvested at day10-replicate2.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt

value: Poly-miR at day8


title: Hs_H1_WT_D8-10-miR-poly_RNAseq_1

description:
RNA-seq of PP cells transduced with Poly-miR at day8 and harvested at day10-replicate1.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt


title: Hs_H1_WT_D8-10-mIR127_RNAseq_2

description:
RNA-seq of PP cells transduced with miR-127 at day8 and harvested at day10
mir127_FPKM_log2_nozeros.txt

data_processing:
Reads were aligned to the hg19 by STAR with parameters: --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --runThreadN 5.Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: gene expression data table in text format

extract_protocol:
mRNA was extracted using miReasy mini kit from Qiagen.
Libraries were prepared using the protocol from Dr. Sander lab. Briefly, RNA were first poly A selected and then subject to RNA fragmentation. Then fragmented RNA were proceeded with first stand synthesis, second strand synthesis, end repair and A-tailing. Resulting product was ligated with adaptor and selected by size, and next were enriched using PCR. At last DNA purification was performed and samples sent out for sequencing.

tag: tissue

value: Endocrine

value: miR-127 at day8 and harvested at day10


title: Hs_H1_WT_D8-10-Let-7a_RNAseq_2

description:
RNA-seq of PP cells transduced with Let-7a loop mutant at day8 and harvested at day10-replicate2.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt

value: Let-7a loop mutant at day8


title: Hs_H1_WT_D8-10-miR-375_RNAseq_1

description:
RNA-seq of PP cells transduced with miR-375 at day8 and harvested at day10-replicate1.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt


title: Hs_H1_WT_D8-10-EV_RNAseq_2

description:
RNA-seq of PP cells transduced with empty vector control at day8 and harvested at day10-replicate2.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt


title: Hs_H1_WT_D8-10-miR-200a_RNAseq_1

description:
RNA-seq of PP cells transduced with miR-200a at day8 and harvested at day10-replicate1.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt


title: Hs_H1_WT_D8-10-Let-7g_RNAseq_2

description:
RNA-seq of PP cells transduced with Let-7g loop mutant at day8 and harvested at day10-replicate2.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt

value: Let-7g loop mutant at day8


title: Hs_H1_WT_D8-10-Let-7a_RNAseq_1

description:
RNA-seq of PP cells transduced with Let-7a loop mutant at day8 and harvested at day10-replicate1.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt


title: Hs_H1_WT_D8-10-Let-7g_RNAseq_1

description:
RNA-seq of PP cells transduced with Let-7g loop mutant at day8 and harvested at day10-replicate1.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt


title: Hs_H1_WT_D8-10-EV_RNAseq_1

description:
RNA-seq of PP cells transduced with empty vector control at day8 and harvested at day10-replicate1.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt


title: methylation_BHB_low_vs_high_1_dyeswap

type: genomic

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description:
Biological replicate 3 of 4
Array 3

hyb_protocol: Hybridizations were performed according to the microarray manufacturer’s instructions (Agilent Technologies). Briefly, 1.4 μg of labeled sample (in 40 μL) was mixed with 158 μL of hybridization master mix containing 25 μL of Bovine Hybloc competitor DNA (1 mg/ml) , Applied Genetics Laboratories), 2.6 μL of Agilent 100x Blocking Agent and 130 μL of Agilent 2× HI-RPM Hybridization Buffer (Agilent Technologies). Samples were held at 95°C for 3 min and at 37°C for 30 min followed by addition of 65 μL of Agilent-CGHBlock (final volume 260 μL). The samples were loaded onto the microarray and hybridization was carried out in a hybridization oven (Shel Lab) for 40 h at 65°C and 20 rpm. Washing was carried out according to the microarray manufacturer’s instructions

scan_protocol: Scan on a PowerScanner (Tecan) at 2um using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing:
The array data analysis methods and downstream analysis pipelines are described in detail in (Saadi et al., 2014). Briefly, after Loess normalization, quantile inter-array scale normalization was performed and fitted to a linear model and thus, Bayesian statistics of differential expression were obtained. Thus, differentially methylated probes were identified using linear models for microarray data (LIMMA).
The processed data file contains log2 normalized  Cy5/Cy3 ratios for all probes including controls.

organism: Bos taurus

source_name: morulas+blastocysts BHB_low_3

label_protocol: For each sample, 2 μg of DNA was labeled using the Universal Linkage System (ULS) labeling kit (Kreatech Biotechnology) according to the manufacturer’s instructions with minor modifications: 1 μL of Cy-ULS dye was added per 1 μg of genomic DNA adjusted with 10× labeling buffer. The labelling mixture was then held for 30 min at 85°C in a thermocycler, followed by 3 min on ice. Non-reacted ULS-Cy3/5 was removed by purification using a QIAquick PCR Purification Kit and samples were eluted in 23.5 μL nuclease-free water. A 1.5 μL aliquot was used to determine DNA concentration and dye incorporation using the ND- 1000 NanoDrop.

extract_protocol:
Animal selection: Two groups of cow were selected, 1- BHB_low consisted of cows considered weakly affected by a metabolic disorder (systemic concentration under 0.9 mmol/l of Beta-Hydroxybutyrate) . 2-BHB_high  consisted of cows highly affected by a negative energetic balance (systemic concentration over 0.9 mmol/l of Beta-Hydroxybutyrate)
Ovarian stimulation: The start of the ovulation schedule is between days 8 and 14 of the oestrous cycle. Two days before the start of the injections, the dominant follicle is aspirated transvaginally to begin a follicular wave.  The ovarian stimulation program consisted of eight injections of 400 mg FSH (Folltropin-V, Bioniche Animal Health, Belleville, ON, Canada) administered at 12 hr intervals. Then 500 µm of cloprostenol (Estrumate, Merck Animal Health, Madison, NJ, United State) was injected with the sixth injection of FSH. Oestrus occurs five days after the start of the injections (Day 6 of the super-stimulation schedule). Cattles were then inseminated with four doses of sexed semen from six bulls (Centre d’Insémination Artificielle du Québec, St-Hyacinthe, QC, Canada); two doses in the afternoon of the sixth day and two in the morning of the seventh day. Embryos were collected seven days after the beginning of the estrus.
Total RNA and gDNA were extracted using the AllPrep DNA/RNA Micro Kit (Qiagen)
amp protocol: The methodology have been thoroughly describef in (Saadi et al., 2014). Briefly, 10ng of DNA sample and spike-in control were cut in ≈160bp fragment using MSEI restriction enzyme. MseLig 12 and MseLig 21 adapters were added to the fragmented gDNA sites. Sample were the digested using methyl sensitive restriction enzyme HpaII, HinP1I and AciI. Only unmethylated fragment have been targeted by those enzyme, leaving only one adapter on the cleaved fragment. Efficiency of the digestion was confirmed by analyzing the spike-in control added prior to the DNA fragmentation step. For the step, qPCR was performed by preparing a separate mixes containing forward and reverse primer targeting HpaII, HinP1I and AciI site. Undigested spike-in (1/1000 dilution) was used as a positive control and non-template controls were also added as negatives control. The amplification plot and the dissociation curve were evaluated for each primer set separately. The DNA fragmentation was considered successful when the threshold cycle (ct) was greater than 5 when compared to the undigested control.Fragment selection by ligation-mediated PCR After cleavage by methyl sensitive enzyme, the gDNA was purified by ethanol precipitation and dissolve in nuclease free water. Selective amplification of methylated fragments was performed using two rounds of ligation-mediated PCR (LM-PCR). The PCR products were resolved on 0.8% agarose gel to assess the quality. Then the previously added linker were removed.

value: morulas+blastocysts

source_name: morulas+blastocysts BHB_high_3


title: methylation_BHB_high_vs_low_2

description:
Biological replicate 2 of 4
Array 2

source_name: morulas+blastocysts BHB_high_2

source_name: morulas+blastocysts BHB_low_2


title: methylation_BHB_low_vs_high_2_dyeswap

description:
Biological replicate 4 of 4
Array 4

source_name: morulas+blastocysts BHB_low_4

source_name: morulas+blastocysts BHB_high_4


title: methylation_BHB_high_vs_low_1

description:
Biological replicate 1 of 4
Array 1

source_name: morulas+blastocysts BHB_high_1

source_name: morulas+blastocysts BHB_low_1


title: islet_RNA-Seq_rep3

description: RNA-seq of human cadaveric islet-replicate3

data_processing:
Reads were aligned to the hg19 by STAR with parameters: --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --runThreadN 5.Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: gene expression data table in text format

source_name: human cadaveric islet

growth_protocol: Human cadaveric islet cells were directly isolated from donors.

extract_protocol:
RNA was extracted using Qiagen Rneasy kit
Libraries were prepared using the protocol from Frazer lab. Briefly, RNA were first poly A selected and then subject to RNA fragmentation. Then fragmented RNA were proceeded with first stand synthesis, second strand synthesis, end repair and A-tailing. Resulting product was ligated with adaptor and selected by size, and next were enriched using PCR. At last DNA purification was performed and samples sent out for sequencing.

treatment_protocol: Human islet was washed with culture medium, collected and lysed in Trizol

value: a mixture of alpha, beta, delta, PP cells

tag: development stage

value: fully differentiated

value: endocrine tissue


title: islet_RNA-Seq_rep2

description: RNA-seq of human cadaveric islet-replicate2


title: PC3-PBS rep 1

city: Woolloongabba

first: Inge

last: Seim

state: Queensland

address: 37 Kent St

country: Australia

institute: Queensland University of Technology

description:
PC3-PBS-1
polyadenylated RNA
mRNA-Seq
stranded

data_processing:
Pre-processing of raw FASTQ reads, including elimination of contaminating adapters, was performed with scythe v0.994 (https://github.com/vsbuffalo/scythe).
Mouse reads were filtered from xenograft samples prior to alignment using Xenome v1.0.1 [22689758].
FASTQ files were aligned to the human genome, build hg19 downloaded from the Illumina iGenome resource at http://goo.gl/LspLBZ, using Bowtie2 v2.1.0 [PMID 22388286] and the spliced-read mapper TopHat (v2.0.9) [PMID 23618408] and reference gene annotations to guide the alignment (-G argument in TopHat).
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using a Cufflinks v2.1.1 [PMID 22383036], with default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.fpkm.txt: Tab-delimited text files include FPKM values for each Sample (abundance measurements).

source_name: PC3 xenograft

growth_protocol: The human PCa cell line PC3 (ATCC CRL-1435) was maintained in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen, Mulgrave, VIC, Australia) with 10% New Zealand Cosmic Calf Serum (FCS, Thermo Fisher Scientific Australia, Scoresby, VIC, Australia). All media was supplemented with 100 U/mL penicillin G and 100 ng/mL streptomycin (Invitrogen).

extract_protocol:
At end point, the primary tumour was resected, divided in half, snap frozen and stored at -80°C. Total RNA was extracted from cell pellets using an RNeasy Plus Mini Kit (QIAGEN, Melbourne, Australia) with a genomic DNA (gDNA) Eliminator spin column, according to the manufacturer’s instructions. RNA purity was analysed using the Agilent 2100 Bioanalyzer, and RNA with an RNA integrity number above 7 used for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq stranded mRNA library. TruSeq rapid SBS kit or TruSeq SBS Kit v4).

treatment_protocol: PC3 cells were introduced into 3-week-old male mice (NOD/SCID) (Jackson Laboratories; supplied by the animal Resource Centre, Western Australia). Cells were subcutaneously injected in a 1:1 ratio with a Matrigel into the hind flank region of the mice. Tumours were allowed to grow until a volume of approximately 100mm^3 was reached, when mice were divided into two experimental groups. Mice then received daily intraperitoneal injections of 20 nanomoles/mouse [D-Lys3]-GHRP-6 (Sigma-Aldrich, St-Louis, MO, USA) (n=3) or PBS control (n=3) for 14 days.

tag: xenograft

value: PC3 prostate cancer cell line

tag: mouse host strain

value: NOD/SCID

tag: treatment

value: PBS


title: PC3-DL3 rep 2

description:
PC3-DL3-2
polyadenylated RNA
mRNA-Seq
stranded

value: ghrelin receptor antagonist [D-Lys3]-GHRP-6


title: Sample 37 [sss]

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

description:
Sample 37
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv

data_processing:
Multiplexed samples were demultiplexed using the Illumina software Casava.
Reads were aligned to the human genome (hs_GRCh38.p2) using STAR.
The number of reads mapped within genes was quantified by HTSeq (version HTSeq-0.6.1p1, mode union, strand reverse, quality alignment greater than 10).
Genome_build: hs_GRCh38.p2
Supplementary_files_format_and_content: allSamplesCounts_htseqcov1_sss_forGEO.csv: Comma-separated value file includes counts for each annotated gene (row) for each sample (column).
Supplementary_files_format_and_content: lcpmy1_sss_forGEO.csv: Comma-separated value file includes log2 count per millions after discarding genes low expressed genes (defined as less than an average of 20 counts) and TMM normalization.

source_name: vastus lateralis muscle

extract_protocol:
Lysates were prepared by homogenization using the Qiagen Tissue Lyzer. Nucleic acid recovery from these extracts was by enzymatic digestion and/or spin-column purification using standard approaches.
Illumina TruSeq Stranded RNA Ribo Zero Gold Kit.

tag: population

value: Chinese descent

tag: sarcopenia status

value: yes

tag: Sex

value: male

tag: age (yr)

value: vastus lateralis muscle


title: Sample 38 [sss]

description:
Sample 38
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv

value: no


title: Sample 40 [sss]

description:
Sample 40
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: PC3-PBS rep 2

description:
PC3-PBS-2
polyadenylated RNA
mRNA-Seq
stranded


title: PC3-DL3 rep 1

description:
PC3-DL3-1
polyadenylated RNA
mRNA-Seq
stranded


title: PC3-PBS rep 3

description:
PC3-PBS-3
polyadenylated RNA
mRNA-Seq
stranded


title: islet_RNA-Seq_rep1

description: RNA-seq of human cadaveric islet-replicate1


title: Sample 39 [sss]

description:
Sample 39
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: library enriched for miRNAs in RISC complex

city: Munich

first: Carolin

last: Daniel

address: Heidemannstrasse 1

country: Germany

institute: Helmholtz Zentrum München

description: miRNA

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
Adapter trimming and alignment to genome, RefSeq, and miRNA hairpins, using ungapped alignment with bowtie.
Collapsing reads on RefSeq sequences to create Ago footprints
Adapter trimming and alignment to RefSeq with STAR followed by alingment of dangling ends to miRNA hairpins using bowtie
Genome_build: hg19
Genome_build: RefSeq 2012
Supplementary_files_format_and_content: rna-footprints.bed: Locations of concentrations of read starting points in RISC occupancy on RefSeq RNAs.  BED format with score indicating reads within each peak
Supplementary_files_format_and_content: miRNA-RISC-Complex-Frequcency.tsv: Frequency of miRNAs in the RISC-complex in tab-delimited format. BED-like
Supplementary_files_format_and_content: chimeric.mirna.bed: Locations of chimeric mRNA/miRNA reads on RefSeq RNAs in BED format.  The feature name is the miRNA, the score is the number of reads

source_name: T-cell

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from fresh venous blood by density gradient centrifugation using Ficoll-Paque PLUS (GE Healthcare). CD4+ T cells were purified from PBMCs by Magnetic Activated Cell Sorting (MACS) using CD4 microbeads (Miltenyi Biotec) following the manufacturers protocol.

extract_protocol:
HITS-CLIP was performed according to the method of Chi et al. (PMID: 19536157) with slight modification. Briefly, human CD4 + T cells were subjected to UV-crosslinking three times at 400 mJ/cm². Cells were then lysed and treated sequentially with DNase and RNase T1. The Argonaute complex was then immunoprecipitated 2-4 hours at 4°C using the monoclonal Argonaute antibody 2A8. After on-bead ligation of a 3' linker, Ago2-RNA complexes were isolated by SDS gel electrophoresis and RNA was extracted. 5' RNA linkers were then ligated to the RNA sample. RNA molecules with 5' and 3' linkers were amplified by RT/PCR, and the resulting products were separated on agarose gel. Two respective populations of RNA (50-60bp for small RNAs, 80-180bp for mRNAs) were extracted. A second round of PCR using Solexa Fusion primers was performed and products were purified by gel extraction, analyzed on an Agilent Bioanalyzer, and  subjected to sequencing on an Illumina Hi-Seq 2000. The readouts were preprocessed and mapped to the human genome (UCSC hg19 assembly) and potential miRNA-mRNA pairs were predicted using the miRanda program (v3.3a).
Ago2-bound mRNA and miRNA sequencing libraries were derived based on the method of Chi SW, et al. [PMID: 19536157].
HITS-CLIP

tag: marker


title: library enriched for mRNA (chimeric) fragments of RISC complex

description: mRNA


title: Sample 33 [sss]

description:
Sample 33
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 36 [sss]

description:
Sample 36
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 35 [sss]

description:
Sample 35
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 34 [sss]

description:
Sample 34
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 32 [sss]

description:
Sample 32
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 29 [sss]

description:
Sample 29
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: PC3-DL3 rep 3

description:
PC3-DL3-3
polyadenylated RNA
mRNA-Seq
stranded


title: Sample 31 [sss]

description:
Sample 31
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 30 [sss]

description:
Sample 30
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 28 [sss]

description:
Sample 28
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 27 [sss]

description:
Sample 27
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 24 [sss]

description:
Sample 24
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 23 [sss]

description:
Sample 23
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 25 [sss]

description:
Sample 25
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 22 [sss]

description:
Sample 22
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 26 [sss]

description:
Sample 26
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 14 [sss]

description:
Sample 14
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 21 [sss]

description:
Sample 21
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 15 [sss]

description:
Sample 15
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 18 [sss]

description:
Sample 18
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 17 [sss]

description:
Sample 17
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 16 [sss]

description:
Sample 16
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 11 [sss]

description:
Sample 11
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 9 [sss]

description:
Sample 9
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 13 [sss]

description:
Sample 13
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 10 [sss]

description:
Sample 10
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 12 [sss]

description:
Sample 12
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 5 [sss]

description:
Sample 5
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 8 [sss]

description:
Sample 8
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 7 [sss]

description:
Sample 7
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 39 [jss]

description:
Sample 39
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv

data_processing:
Multiplexed samples were demultiplexed using the Illumina software Casava.
Reads were aligned to the human genome (hs_GRCh38.p2) using STAR.
The number of reads mapped within genes was quantified by HTSeq (version HTSeq-0.6.1p1, mode union, strand reverse, quality alignment greater than 10).
Genome_build: hs_GRCh38.p2
Supplementary_files_format_and_content: allSamplesCounts_htseqcov1_jss_forGEO.csv: Comma-separated value file includes counts for each annotated gene (row) for each sample (column).
Supplementary_files_format_and_content: lcpmy1_jss_forGEO.csv: Comma-separated value file includes log2 count per millions after discarding genes low expressed genes (defined as less than an average of 20 counts) and TMM normalization.

value: Afro-Caribbean descent

tag: low muscle mass

tag: low muscle strength and/or low physical performance


title: Sample 6 [sss]

description:
Sample 6
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 1 [sss]

description:
Sample 1
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 4 [sss]

description:
Sample 4
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 38 [jss]

description:
Sample 38
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 3 [sss]

description:
Sample 3
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 19 [sss]

description:
Sample 19
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 35 [jss]

description:
Sample 35
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 31 [jss]

description:
Sample 31
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 36 [jss]

description:
Sample 36
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 34 [jss]

description:
Sample 34
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 32 [jss]

description:
Sample 32
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 37 [jss]

description:
Sample 37
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 33 [jss]

description:
Sample 33
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 30 [jss]

description:
Sample 30
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 27 [jss]

description:
Sample 27
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 28 [jss]

description:
Sample 28
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 24 [jss]

description:
Sample 24
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 26 [jss]

description:
Sample 26
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 22 [jss]

description:
Sample 22
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 20 [sss]

description:
Sample 20
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 20 [jss]

description:
Sample 20
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 2 [sss]

description:
Sample 2
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_sss_forGEO.csv


title: Sample 19 [jss]

description:
Sample 19
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 14 [jss]

description:
Sample 14
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 21 [jss]

description:
Sample 21
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 15 [jss]

description:
Sample 15
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 18 [jss]

description:
Sample 18
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 11 [jss]

description:
Sample 11
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 16 [jss]

description:
Sample 16
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 13 [jss]

description:
Sample 13
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 12 [jss]

description:
Sample 12
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 29 [jss]

description:
Sample 29
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 23 [jss]

description:
Sample 23
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 25 [jss]

description:
Sample 25
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 10 [jss]

description:
Sample 10
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 9 [jss]

description:
Sample 9
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 4 [jss]

description:
Sample 4
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 8 [jss]

description:
Sample 8
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 5 [jss]

description:
Sample 5
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 2 [jss]

description:
Sample 2
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 7 [jss]

description:
Sample 7
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 3 [jss]

description:
Sample 3
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 39 [hss]

description:
Sample 39
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv

data_processing:
Multiplexed samples were demultiplexed using the Illumina software Casava.
Reads were aligned to the human genome (hs_GRCh38.p2) using STAR.
The number of reads mapped within genes was quantified by HTSeq (version HTSeq-0.6.1p1, mode union, strand reverse, quality alignment greater than 10).
Genome_build: hs_GRCh38.p2
Supplementary_files_format_and_content: allSamplesCounts_htseqcov1_hss_forGEO.csv: Comma-separated value file includes counts for each annotated gene (row) for each sample (column).
Supplementary_files_format_and_content: lcpmy1_hss_forGEO.csv: Comma-separated value file includes log2 count per millions after discarding genes low expressed genes (defined as less than an average of 20 counts) and TMM normalization.

extract_protocol:
mirVana miRNA Isolation Kit (Life Technologies).
Illumina TruSeq Stranded RNA Ribo Zero Gold Kit.

value: Caucasian descent


title: Sample 17 [jss]

description:
Sample 17
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 38 [hss]

description:
Sample 38
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 31 [hss]

description:
Sample 31
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 34 [hss]

description:
Sample 34
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 32 [hss]

description:
Sample 32
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 37 [hss]

description:
Sample 37
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 30 [hss]

description:
Sample 30
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 35 [hss]

description:
Sample 35
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 33 [hss]

description:
Sample 33
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 24 [hss]

description:
Sample 24
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 27 [hss]

description:
Sample 27
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 29 [hss]

description:
Sample 29
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 26 [hss]

description:
Sample 26
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 28 [hss]

description:
Sample 28
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 23 [hss]

description:
Sample 23
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 22 [hss]

description:
Sample 22
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 21 [hss]

description:
Sample 21
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 40 [hss]

description:
Sample 40
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 1 [jss]

description:
Sample 1
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 6 [jss]

description:
Sample 6
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_jss_forGEO.csv


title: Sample 18 [hss]

description:
Sample 18
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 17 [hss]

description:
Sample 17
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 36 [hss]

description:
Sample 36
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 12 [hss]

description:
Sample 12
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 15 [hss]

description:
Sample 15
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 13 [hss]

description:
Sample 13
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 25 [hss]

description:
Sample 25
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 11 [hss]

description:
Sample 11
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 7 [hss]

description:
Sample 7
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 10 [hss]

description:
Sample 10
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 9 [hss]

description:
Sample 9
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 8 [hss]

description:
Sample 8
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 3 [hss]

description:
Sample 3
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 2 [hss]

description:
Sample 2
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: ND501

city: San Francisco

first: Ling

last: Bai

address: 1550 4th St., Rock Hall Rm 346

department: Physiology

institute: UCSF

description:
NGT_all_R1_RPKM_nocap_sg.csv
Vagal_TargetSeq

data_processing:
all samples: HighSeq 4000 were used for sequecing and de-multiplexed to generate a fastq file.
For Sample 1: De-multiplexing alignment to the mm10 transcriptome and unique molecular identifier (UMI)-collapsing were performed using Cell Ranger version 2.0.1, available from 10x Genomics with default parameters.
For all other samples: Reads were aligned to annotated mRNAs in the mouse genome (UCSC, Mus musculus assembly mm10) and the read count for each gene was calculated using ArrayStar software (DNAstar).
Genome_build: mm10
Supplementary_files_format_and_content: mtx file generated by Cell Ranger v2.0.1, including all cells in Sample 1
Supplementary_files_format_and_content: csv file include reads values for all cells (ND1-501) other than sample 1

organism: Mus musculus

source_name: Nodose ganglion cells

extract_protocol:
Nodose ganglion cells are dissociated using a combination of papain/collagenase/dispase solution. 10x Genomics (Sample 1) or Smart-Seq 2 (all other samples) was used to prepare cDNA library
Sequencing library is prepared follow the instruction of 10x Genomics (Sample 1) or using Nextera DNA Library Prep Kit (all other samples)

tag: strain

value: nodose ganglion

tag: age

value: post natal 8-12 weeks

tag: genotype

value: wild type


title: Sample 4 [hss]

description:
Sample 4
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 1 [hss]

description:
Sample 1
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: ND500


title: ND499


title: Sample 19 [hss]

description:
Sample 19
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: ND498


title: ND497


title: ND494


title: Sample 20 [hss]

description:
Sample 20
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: ND495


title: ND496


title: ND493


title: ND492


title: Sample 14 [hss]

description:
Sample 14
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 16 [hss]

description:
Sample 16
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: ND491


title: Sample 6 [hss]

description:
Sample 6
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: Sample 5 [hss]

description:
Sample 5
rRNA-depleted RNA-seq
Processed data file: allSamplesCounts_htseqcov1_hss_forGEO.csv


title: ND487


title: ND488


title: ND489


title: ND490


title: ND486


title: ND484


title: ND485


title: ND483


title: ND481


title: ND480


title: ND482


title: ND476


title: ND477


title: ND475


title: ND473


title: ND471


title: ND474


title: ND469


title: ND466


title: ND472


title: ND467


title: ND465


title: Summer Delight before rep3

city: Fredericton

first: Martin

last: Lague

state: New Brunswick

address: 850 Lincoln Rd.

institute: Agriculture and Agri-Food Canada

data_processing:
Genome alignment and expression analysis was performed using the same protocol as outlined in (Gálvez et al. 2016). Reads were aligned to the S. tuberosum reference genome v3_2.1.10 (Potato Genome Sequencing Consortium 2011) using TopHat software suite v. 2.0.9 (Kim et al. 2013) with the “fr-unstranded” library type option. Quality of alignments was verified using the ‘flagstat’ tool from SAMtools v. 0.1.19 (Li et al. 2009).
Transcripts were assembled using CuffLinks v. 2.1.1 (Trapnell et al. 2012), based on the S. tuberosum ITAG1.0 transcript dataset (Fernandez-Pozo et al. 2015, Tomato Genome Consortium 2012). Transcriptome assembly was performed with ‘multi read correct’ and ‘fragment bias correct’ options enabled. Assembled transcripts from different replicates were merged into a single reference transcriptome CuffMerge included in CuffLinks. From the analysis an FPKM value was obtained for each gene in all 10 sequenced cultivars.
Genome_build: S. tuberosum reference genome v3_2.1.10 (Potato Genome Sequencing Consortium 2011)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (cuffdiff output)

organism: Solanum tuberosum

source_name: tuber

extract_protocol:
Sampling was done with freshly harvested tubers (within two weeks of harvest) before cold storage and tubers after cold storage.   Each tuber was sampled once at either end and three times around the middle for a total of five cores per tuber in regions without eyes. For each replicate the cores from three tubers were pooled in 50 ml Falcon tubes. This results in 15 cores from three tubers per replicate.  Three replicates were taken from each clone for a total of nine tubers per clone. Tuber cores were flash frozen in liquid nitrogen and freeze-dried. Two 5/32” stainless steel balls (MP Biomedicals) were added to tubes containing tuber cores and the tuber cores were ground to a powder using Geno/Grinder (SPEX, Metuchen, U. S. A.) at 500(1X), for 2 minutes. Freeze-dried tuber powder was then stored at room temperature. The same tuber powder was used for both glucose determination and RNA extraction. RNA extraction from freeze-dried tuber tissue was performed using an Agencourt RNAdvance Tissue kit with  modifications (Tai et al. 2013). One ml Hot Borate buffer (200mM sodium borate decahydrate (Borax) pH 9.0, 30mM EGTA, 1% (w/v) SDS, 1% (w/v) sodium deoxycholate, and, added just before use, 10mM dithiothreitol and 2%(w/v) PVP (MW 40,000)) were added to 150 mg freeze-dried tuber core powder and the sample was homogenized using a vortex. The samples were centrifuged for 5 minutes at 10,000rpm and 200μl of the supernatant was transferred to a 96-well plate. The remaining sample was frozen at -80°C. To the samples in the 96-well plate 10μl of Agencourt proteinase K solution was added and the samples were mixed gently by pipetting up and down. Following addition of Agencourt proteinase K solution the samples were incubated at 37°C for 25 minutes. At this point the protocol followed the standard automated Agencourt RNAdvance Tissue kit with the Beckman Counter BioMek NXp workstation.
Libraries were generated using the TruSeq RNA kit (Illumina). Messenger RNA was purified from 1 mg of total RNA using oligo-dT beads. The mRNA enriched fraction was reverse transcribed to generate cDNA fragments that were sheared to yield ~200 bp fragments. Following end-repair, 3’ end adenylation steps, and index ligation, a PCR amplification step was performed. There were three biological replicates for each of the cultivars generating a total of 30 samples. A separate index was used for each cultivar-replicate combination. The quality of the library was assessed on a DNA 1000 chip and quantified by qPCR. Libraries were subjected to 100 bases of sequencing on a HiSeq 2000 (Illumina) instrument in paired-end mode. Initial quality control of the data was performed using the software included with the sequencer.

treatment_protocol: cold storage at 4°C for 3 months

tag: cultivar

value: Summer Delight

tag: sampling time

value: freshly harvested


title: Summer Delight before rep2


title: Summer Delight before rep1


title: ND468

tag: tissue


title: ND463


title: ND462


title: ND460


title: Summer Delight after rep2

value: after 3 months of cold storage at 4°C


title: ND461


title: Summer Delight after rep3


title: Summer Delight after rep1


title: Shepody before rep2

value: Shepody


title: ND464


title: ND457


title: ND458


title: Shepody before rep1


title: ND455


title: ND456


title: Shepody after rep2


title: ND454


title: Lady Claire before rep3

value: Lady Claire


title: Lady Claire before rep2


title: ND453


title: Lady Claire before rep1


title: ND452


title: ND450


title: Lady Claire after rep3


title: Lady Claire after rep2


title: ND448


title: ND447


title: ND444


title: Shepody after rep3


title: Lady Claire after rep1


title: ND445


title: Karaka before rep1

value: Karaka


title: ND443


title: Karaka after rep2


title: Shepody after rep1


title: Karaka after rep3


title: Doremi before rep3

value: Doremi


title: ND440


title: ND439


title: ND438


title: Doremi before rep1


title: ND451


title: ND437


title: Doremi after rep3


title: Shepody before rep3


title: Doremi after rep2


title: ND435


title: ND459


title: Doremi after rep1


title: Karaka before rep2


title: ND446


title: Karaka before rep3


title: ND432


title: Karaka after rep1


title: Crop-20 before rep2


title: ND433


title: ND430


title: ND431


title: ND429


title: Crop-20 after rep3


title: Crop-20 after rep2


title: Doremi before rep2


title: ND428


title: ND427


title: ND436


title: ND426


title: ND425


title: ND442


title: 575.04.1 before rep2


title: 575.04.1 before rep3


title: 575.04.1 before rep1


title: 575.04.1 after rep2


title: ND424


title: 575.04.1 after rep3


title: ND422


title: ND423


title: Crop-20 before rep3


title: Crop-20 before rep1


title: ND421


title: ND420


title: ND419


title: Crop-20 after rep1


title: ND417


title: 15328-26 before rep3


title: 15328-26 before rep2


title: 15328-26 after rep2


title: 15328-26 after rep3


title: 575.04.1 after rep1


title: ND415


title: ND416


title: 15328-26 after rep1


title: 15323-04 before rep3


title: ND414


title: 15328-26 before rep1


title: 15323-04 before rep1


title: ND413


title: ND411


title: 15323-04 before rep2


title: 15323-04 after rep3


title: ND410


title: ND409


title: 15323-04 after rep2


title: ND408


title: 15323-04 after rep1


title: ND407


title: 15329-03 before rep3


title: 15329-03 before rep2


title: ND418


title: ND406


title: 15329-03 before rep1


title: 15329-03 after rep3


title: 15329-03 after rep2


title: ND404


title: ND403


title: ND402


title: ND401


title: Bone irradiation EC Rep3

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

description:
whole bone GFP+ cells
BM_EC_9GY_fpkms.txt
9GY-3

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
Tophat (v2.1.1) used for alignment
HTSeq-count (v0.6.1) used for transcriptome abundance measurement
DESeq2(v1.18.1) used for differential gene expression analyses
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Femur/Tibia

extract_protocol:
Adult mouse bone samples were crashed with pestle, treated with collagenase IV, and digested to single cells. These single cell suspension were stained for FACS sorting. FACS sorted cell population were directly lysis into RLT buffer and RNA were extracted using RNeasy plus Micro Kit (Qiagen)
Double strand cDNA was synthesized using SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara) and sequencing library was constructed with Nextera XT DNA Library preparation kit (illumina). TruSeq Stranded Total RNA kit (Illumina) was used for the library preparation of total BMC and Lin- samples.

value: 9 Gy irradiation

value: 8-12 weeks


title: Bone irradiation EC Rep2

description:
whole bone GFP+ cells
BM_EC_9GY_fpkms.txt
9GY-2


title: 15329-03 after rep1


title: ND398


title: Bone irradiation EC Rep1

description:
whole bone GFP+ cells
BM_EC_9GY_fpkms.txt
9GY-1


title: ND396


title: ND395


title: Bone EC Rep3

description:
whole bone GFP+ cells
BM_EC_9GY_fpkms.txt
EC-3


title: ND397


title: Bone EC Rep2

description:
whole bone GFP+ cells
BM_EC_9GY_fpkms.txt
EC-2


title: Bone EC Rep1

description:
whole bone GFP+ cells
BM_EC_9GY_fpkms.txt
EC-1


title: LSK Rep3

description:
whole bone Lin-Sca1+cKit+ cells
BM_EC_9GY_fpkms.txt
LSK-3

value: wildtype


title: ND393


title: LSK Rep2

description:
whole bone Lin-Sca1+cKit+ cells
BM_EC_9GY_fpkms.txt
LSK-2


title: ND394

description:
NGT_all_R1_RPKM_nocap_sg.csv
Vagal_TargetSeq


title: LSK Rep1

description:
whole bone Lin-Sca1+cKit+ cells
BM_EC_9GY_fpkms.txt
LSK-1


title: ND390


title: Lin- Rep2

description:
whole bone lineage negative cells
BM_EC_9GY_fpkms.txt
Lin-2


title: Lin- Rep3

description:
whole bone lineage negative cells
BM_EC_9GY_fpkms.txt
Lin-3


title: ND391


title: Lin- Rep1

description:
whole bone lineage negative cells
BM_EC_9GY_fpkms.txt
Lin-1


title: ND399


title: ND389


title: ND388


title: BMC Rep3

description:
whole bone marrow cells
BM_EC_9GY_fpkms.txt
BMC-3


title: BMC Rep2

description:
whole bone marrow cells
BM_EC_9GY_fpkms.txt
BMC-2


title: ND387


title: ND386


title: BMC Rep1

description:
whole bone marrow cells
BM_EC_9GY_fpkms.txt
BMC-1


title: ND385


title: ND384


title: ND383


title: ND392


title: ND382


title: ND381


title: Epithelial cells_2

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dymanics Research

country: Japan

institute: RIKEN

description: rep1-3: independent library preparations; A,B: different sequencing run for the same library

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assembly using TopHat2
Mapped reads seperated by genes, and the reads mapped for each gene were clustered by molecular barcode
The number of clusters for each was counted, which provides the number of molecules detected for each gene
The copy number of RNA molecules per cell for each gene is calculated based on spike-in RNA detection efficiency
Genome_build: mm10
Supplementary_files_format_and_content: The calculated copy number of RNA molecules per cell for each gene

source_name: Epithelial cells

extract_protocol:
RNAs from cell lysate obtained by heat elevation is directly used for the next RT reaction
Libraries were prepared by using molecular barcoding technique. First, for normalization, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains 100 cells. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: GP2+ and GP2- cells were isolated from EpCAM+CD45-CD24-cells by using FACS.

tag: cell type

value: Epithelial cells

tag: cell markers


title: Epithelial cells_1


title: Epithelial cells_3


title: M cells_2

source_name: M cells

value: M cells


title: ND380


title: ND379


title: M cells_3


title: M cells_1


title: ND378


title: ND375


title: ND376


title: ND374


title: ND371


title: Abcb1a-EGFP/Rpl10a-ES3026; Input1 (JL)

city: New York

first: Eric

middle: F

last: Schmidt

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
library strategy: TRAP-seq
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

source_name: Abcb1a-EGFP/Rpl10a-ES3026; Input_JL

extract_protocol:
The cerebral cortex was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: Control mice only. No treatment

tag: genotype/variation

value: Abcb1a-TRAP ES3026

value: Cerebral cortex

value: endothelial cells

tag: molecule subtype

value: Input; total RNA


title: ND373

value: nodose ganglion

value: post natal 8-12 weeks

value: wild type


title: Abcb1a-EGFP/Rpl10a-ES3026; IP1 (JL)

source_name: Abcb1a-EGFP/Rpl10a-ES3026; IP_JL

value: Immunopurified (IP); Ribosomal-bound RNA


title: Abcb1a-EGFP/Rpl10a-ES3026; Input2 (JL)


title: Abcb1a-EGFP/Rpl10a-ES3026; IP3 (JL)


title: Abcb1a-EGFP/Rpl10a-ES3026; IP2 (JL)


title: Abcb1a-EGFP/Rpl10a-ES3026; Input3 (JL)


title: Abcb1a-EGFP/Rpl10a-ES3026; IP3 (ES)

source_name: Abcb1a-EGFP/Rpl10a-ES3026; IP_ES


title: ND370


title: Abcb1a-EGFP/Rpl10a-ES3026; IP2 (ES)


title: ND369


title: Abcb1a-EGFP/Rpl10a-ES3026; IP1 (ES)


title: ND368


title: 96_high fat_30C_iWAT

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

institute: Technical University of Munich

data_processing:
Sequencing software: HiSeq Control Software 2.2.58 Image analysis and base calling: Real-Time Analysis (RTA) 1.18.64 fastq-file generation: CASAVA BCL2FASTQ Conversion Software 1.8.3
Sequenced reads with masked adaptor sequence were mapped to the murine genome, NCBI build 38, by the Genomatix Mapper 3.7.6 (Genomatix Mining Station, settings: 'deep', min. quality 92%).
Unique hits were subjected to expression analysis for RNA-seq (Genomatix Genome Analyzer, ElDorado version 12-2013) and provided as reads per kilobase of exon per megabase of library size (RPKM).
Genome_build: murine NCBI genome build 38
Supplementary_files_format_and_content: tab-delimited text file providing RPKM values for each sample.

source_name: iWAT

extract_protocol:
Deep-frozen iBAT and iWAT was homogenized in 1 ml TRIsure (Bioline, London/UK) and RNA isolated. Further purification of RNA was conducted with the SV Total RNA Isolation System (Promega, Fitchburg WI/USA).
Libraries were constructed from total RNA (TruSeq Stranded mRNA Library Prep, Cat.No. 20020595, Illumina, San Diego CA/USA).

tag: gender

value: male

tag: diet

value: high fat

tag: temperature

value: iWAT


title: ND367


title: 95_high fat_30C_iWAT


title: 94_high fat_30C_iWAT


title: 93_high fat_30C_iWAT


title: ND364


title: ND366


title: ND362


title: ND365


title: 91_high fat_30C_iWAT


title: 90_high fat_30C_iWAT


title: ND363


title: 89_high fat_30C_iWAT


title: ND361


title: ND360


title: 88_high fat_30C_iWAT


title: 87_high fat_30C_iWAT


title: ND358


title: ND359


title: 86_high fat_30C_iWAT


title: 84_high fat_30C_iWAT


title: ND356


title: 85_high fat_30C_iWAT


title: 83_high fat_30C_iWAT


title: ND357


title: 92_high fat_30C_iWAT


title: 82_high fat_30C_iWAT


title: ND354


title: ND355


title: ND352


title: 78_control_30C_iWAT

value: control


title: 80_control_30C_iWAT


title: ND349


title: 77_control_30C_iWAT


title: ND351


title: 79_control_30C_iWAT


title: ND348


title: 76_control_30C_iWAT


title: ND350


title: 75_control_30C_iWAT


title: ND347


title: 74_control_30C_iWAT


title: 73_control_30C_iWAT


title: ND346


title: ND344


title: ND345


title: ND343


title: ND342


title: 72_control_30C_iWAT


title: ND353


title: 70_control_30C_iWAT


title: 71_control_30C_iWAT


title: 69_control_30C_iWAT


title: 81_high fat_30C_iWAT


title: ND341


title: ND340


title: 68_control_30C_iWAT


title: ND339


title: ND338


title: 66_control_30C_iWAT


title: ND337


title: ND335


title: ND336


title: 64_control_20C_iWAT


title: 63_control_20C_iWAT


title: 62_control_20C_iWAT


title: ND333


title: 61_control_20C_iWAT


title: ND332


title: 60_control_20C_iWAT


title: ND331


title: 59_control_20C_iWAT


title: ND329


title: 67_control_30C_iWAT


title: ND328


title: 56_control_20C_iWAT


title: 55_control_20C_iWAT


title: ND327


title: ND326


title: 57_control_20C_iWAT


title: 54_control_20C_iWAT


title: 53_control_20C_iWAT


title: ND324


title: ND325


title: ND334


title: 51_control_20C_iWAT


title: ND322


title: 50_control_20C_iWAT


title: ND320


title: ND321


title: 49_control_20C_iWAT


title: 48_high fat_30C_iBAT

source_name: iBAT

value: iBAT


title: ND330


title: ND318


title: 47_high fat_30C_iBAT


title: 58_control_20C_iWAT


title: ND316


title: 45_high fat_30C_iBAT


title: ND315


title: ND313


title: ND312


title: ND314


title: 44_high fat_30C_iBAT


title: 42_high fat_30C_iBAT


title: 43_high fat_30C_iBAT


title: 52_control_20C_iWAT


title: ND310


title: 41_high fat_30C_iBAT


title: ND311


title: ND319


title: 39_high fat_30C_iBAT


title: ND309


title: 38_high fat_30C_iBAT


title: 37_high fat_30C_iBAT


title: ND317


title: 46_high fat_30C_iBAT


title: 35_high fat_30C_iBAT


title: ND305


title: 34_high fat_30C_iBAT


title: ND303


title: ND304


title: 33_high fat_30C_iBAT


title: ND300


title: ND302


title: 32_control_30C_iBAT


title: 40_high fat_30C_iBAT


title: ND299


title: 31_control_30C_iBAT


title: 30_control_30C_iBAT


title: 29_control_30C_iBAT


title: ND307


title: ND298


title: ND297


title: ND296


title: ND306


title: ND295


title: 27_control_30C_iBAT


title: 28_control_30C_iBAT


title: 26_control_30C_iBAT


title: ND293


title: ND294


title: 36_high fat_30C_iBAT


title: 25_control_30C_iBAT


title: 24_control_30C_iBAT


title: ND292


title: 23_control_30C_iBAT


title: ND291


title: ND290


title: ND289


title: 21_control_30C_iBAT


title: 19_control_30C_iBAT


title: 18_control_30C_iBAT


title: ND287


title: ND286


title: 16_control_20C_iBAT


title: 17_control_30C_iBAT


title: ND283


title: 15_control_20C_iBAT


title: ND284


title: 14_control_20C_iBAT


title: ND282


title: ND281


title: ND288


title: 13_control_20C_iBAT


title: 12_control_20C_iBAT


title: ND279


title: ND280


title: 22_control_30C_iBAT


title: 65_control_30C_iWAT


title: 10_control_20C_iBAT


title: ND277


title: 9_control_20C_iBAT


title: ND278


title: 8_control_20C_iBAT


title: ND276


title: ND275


title: 20_control_30C_iBAT


title: 7_control_20C_iBAT


title: 5_control_20C_iBAT


title: 6_control_20C_iBAT


title: ND273


title: 4_control_20C_iBAT


title: ND271


title: ND272


title: 3_control_20C_iBAT


title: ND269


title: 2_control_20C_iBAT


title: ND270


title: 11_control_20C_iBAT


title: ND268


title: ND262


title: ND265


title: NMR hypoxia rep3

description: polyadenylated RNA

data_processing:
FASTQ files were aligned to rat (NCBI RGSC_v3.4) or NMR (UCSC hetGla2) genomes using Bowtie2 v2.1.0 [PMID 22388286] and the spliced-read mapper TopHat (v2.0.9) [PMID 23618408] and reference gene annotations to guide the alignment (-G argument in TopHat).
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using a Cufflinks v2.1.1 [PMID 22383036], with default parameters.
Insert metrics of PE reads was obtained using picard-tools v1.137 [https://github.com/broadinstitute/picard].
Genome_build: rat NCBI RGSC_v3.4 and NMR UCSC hetGla2
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample (abundance measurements).

molecule: polyA RNA

organism: Heterocephalus glaber

source_name: liver

extract_protocol:
Total RNA was isolated from frozen tissues using an RNAqueous kit (Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Rat and naked mole rats (NMR) were exposed to short-term hypoxia (8% oxygen) for 8 hours --the estimated oxygen condition in NMR tunnels.

value: liver

tag: treatment

value: NMR 8% O2 8 hours


title: ND260


title: NMR hypoxia rep2

description: polyadenylated RNA


title: NMR hypoxia rep1

description: polyadenylated RNA


title: ND274


title: ND258


title: ND256


title: Pancreatic_progenitor_cells_small_RNA-seq

description:
Small RNA-seq of PP cells-replicate 1.
smRNA_seq-Day10
Endocrine tissue
Small RNA

data_processing:
Sequence information was extracted from the image files with the Illumina (San Diego, CA) base calling software package (GAPipeline version 1.4).
Prior to alignment, sequence reads were reduced to a list of only non-redundant (NR) sequences. NR sequences for which a 3′ adapter sequence was observed were truncated up to the junction with the adapter sequence, while sequences without recognizable 3′ adapters were also retained and processed independently.
Reads from the library were preprocessed and mapped to the human genome (UCSC hg19 assembly).
NR-sequences with their genomic coordinates were combined to form the final dataset.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: smRNA_seq-Day10_CyT49.txt: Tab-delimited text file includes miRNA values (RPM).

source_name: Pancreatic progenitor cells

growth_protocol: Pancreatic progenitor stage cells were cultured in DMEM High Glucose supplemented with 1% B-27, 1% of Glutamax, KGF (50 ng/mL) + EGF (50 ng/mL) and incubated at 37˚C and 5% CO2.

extract_protocol:
mRNA was extracted using Qiagen miRNeasy extraction kit.
Libraries were prepared for sequencing using the Illumina protocol Preparing Samples for Analysis of Small RNA (Illumina FC-102-1009).

treatment_protocol: Pancreatic progenitor stage cells were lysed in Trizol and then total RNA was extracted to proceeded to small RNA-seq library preparation.

value: ES-derived pancreatic progenitor cells

tag: es cell line


title: 1_control_20C_iBAT

value: wildtype


title: ND267


title: G648_5 GSC ATAC-seq

city: Toronto

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

institute: SickKids

description:
GSC clone
Raw data file: G648_5_LS11_P6_SF_AT_2_S22_L006_R1_001.fastq.gz

data_processing:
Libraries were sequenced with 50 bp single-end reads which were mapped to hg19 using bowtie2. Reads were filtered to remove duplicates, unmapped or poor quality (Q <30) reads, mitochondrial reads, chrY reads, and those overlapping the ENCODE blacklist.
Following alignment, open chromatin regions/peaks were called using MACS2. Default parameters were used except for the following: --keep-dup all -B --nomodel --SPMR -q 0.05 --slocal 6250 --llocal 6250
The signal intensity featured in the bedgraph files was calculated as the fold enrichment of the signal per million reads in a sample over a modelled local background using the bdgcmp function in MACS2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_peaks.narrowPeak: Called peaks using MACS2, with settings described above.
Supplementary_files_format_and_content: *_sortedFE.bedgraph: bedGraph; signal file produced with MACS2 as described above.

growth_protocol: Cells were cultured adherently under neural stem cell conditions.

extract_protocol: Libraries were constructed as described in Buenrostro et al., Nature Methods, (2013).

value: glioblastoma stem cells


title: ND255


title: ND254


title: ND263


title: gene_expression_BHB_high_vs_low_2

type: RNA

description: Biological replicate 2 of 4

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing:
Signal intensity data files were normalized and analyzed using the FlexArray 1.6.1 software (Genome Quebec, URL: http://genomequebec.mcgill.ca/FlexArray). The first step in the data processing was to remove the background of intensity files using a simple background subtraction. Data were then normalized for dye bias using a within-array loess and a between-array « quantile » normalization to minimize array effects. To calculate fold changes of probe intensity, normalized data were assessed using the e Bayes moderated t-test (LIMMA) included in the FlexArray software. A False Discovery Rate algorithm (Benjamini-Hochberg) was also applied.
The file normalized_log2_Cy5_vs_Cy3_allprobes.txt contains normalized data for all probes including controls. The sample tables do not include data for the control probes.

source_name: morulas+blastocysts BHB_high_2

label_protocol: The labelling aRNA was done using  the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent.

extract_protocol:
Animal selection: Two groups of cow were selected, 1- BHB_low consisted of cows considered weakly affected by a metabolic disorder (systemic concentration under 0.9 mmol/l of Beta-Hydroxybutyrate) . 2-BHB_high  consisted of cows highly affected by a negative energetic balance (systemic concentration over 0.9 mmol/l of Beta-Hydroxybutyrate)
ovarian stimulation: The start of the ovulation schedule is between days 8 and 14 of the oestrous cycle. Two days before the start of the injections, the dominant follicle is aspirated transvaginally to begin a follicular wave.  The ovarian stimulation program consisted of eight injections of 400 mg FSH (Folltropin-V, Bioniche Animal Health, Belleville, ON, Canada) administered at 12 hr intervals. Then 500 µm of cloprostenol (Estrumate, Merck Animal Health, Madison, NJ, United State) was injected with the sixth injection of FSH. Oestrus occurs five days after the start of the injections (Day 6 of the super-stimulation schedule). Cattles were then inseminated with four doses of sexed semen from six bulls (Centre d’Insémination Artificielle du Québec, St-Hyacinthe, QC, Canada); two doses in the afternoon of the sixth day and two in the morning of the seventh day. Embryos were collected seven days after the beginning of the estrus.
Total RNA and gDNA were extracted using the AllPrep DNA/RNA Micro Kit (Qiagen)
amp protocol: Amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Thermo Fisher).

tag: breed

value: Holstein

value: morulas+blastocysts

source_name: morulas+blastocysts BHB_low_2


title: ND253


title: Activated T cells T1D

data_processing:
Adapter trimming: Btrim v0.3.0 (-l15 -3 AGATCGGAAGAGCAC)
Filtering: (rRNA, tRNA) Bowtie v1.2.2 (--best -v1 --norc)
Mapping: Bowtie v1.2.2 (--best -v1 --norc)
Normalization: R-package DESeq2
Genome_build: RNACentral v2; miRBase20
Supplementary_files_format_and_content: readcount list .txt

source_name: T cells (peripheral blood)

extract_protocol:
CD4+ T cells were extracted from peripheral blood using density gradient centrifugation and CD4+ MACS enrichment. CD4+ T cell subpopulations were FACS sorted. RNA was extracted using the miRNeasy Micro Kit (Qiagen).
miRNA libraries were prepared for sequencing using the NEBnext Multiplex Small RNA Library Prep Set (New England Biolabs) according to the manufacturer’s protocol.

value: CD4+ T cell

value: peripheral blood

tag: disease

value: type 1 diabete


title: Naive T cells Control

value: Control


title: Activated T cells Control


title: Naive T cells T1D


title: G648_4 GSC ATAC-seq

description:
GSC clone
Raw data file: G648_4_LS4_P6_SF_AT_1_S4_L001_R1_001.fastq.gz


title: ND259

tag: strain

value: nodose ganglion

value: post natal 8-12 weeks

value: wild type


title: ND261

tag: age


title: ND266

tag: genotype


title: ND252


title: ND251


title: G648_3 GSC ATAC-seq

description:
GSC clone
Raw data file: G648_3_DN14_P6_SF_AT_2_S3_L001_R1_001.fastq.gz


title: ND249


title: gene_expression_BHB_low_vs_high_1_dyeswap

description: Biological replicate 3 of 4

source_name: morulas+blastocysts BHB_low_3

source_name: morulas+blastocysts BHB_high_3


title: gene_expression_BHB_low_vs_high_2_dyeswap

description: Biological replicate 4 of 4

source_name: morulas+blastocysts BHB_low_4

source_name: morulas+blastocysts BHB_high_4


title: ND257

source_name: Nodose ganglion cells


title: G648_1 GSC ATAC-seq

description:
GSC clone
Raw data file: G648_1_CD15_7_P6_SF_AT_1_S25_L007_R1_001.fastq.gz


title: G648_6 GSC ATAC-seq

description:
GSC clone
Raw data file: G648_6_LS17_P6_SF_AT_1_S28_L007_R1_001.fastq.gz


title: ND248


title: gene_expression_BHB_high_vs_low_1

description: Biological replicate 1 of 4

source_name: morulas+blastocysts BHB_high_1

source_name: morulas+blastocysts BHB_low_1


title: ND247


title: ND246


title: G551_DP2 GSC ATAC-seq

description:
GSC clone
Raw data file: G511_DP2_P12_SF_AT_1_CGTACT_L007_R1.fastq.gz


title: G551_1 GSC ATAC-seq

description:
GSC clone
Raw data file: G551_1_SF_AT_2_TCCTGAGC_L001_R1.fastq.gz


title: ND244

description:
NGT_all_R1_RPKM_nocap_sg.csv
Vagal_TargetSeq


title: ND245


title: G648_2 GSC ATAC-seq

description:
GSC clone
Raw data file: G648_2_CD15_8_P8_SF_AT_1_S16_L004_R1_001.fastq.gz


title: G498_7 GSC ATAC-seq

description:
GSC clone
Raw data file: G498_7_SF_AT_2_AGGCAGAA_L001_R1.fastq.gz


title: ND242


title: ND243


title: G551_3 GSC ATAC-seq

description:
GSC clone
Raw data file: G551_3_SF_AT_2_GGACTCCT_L001_R1.fastq.gz


title: G498_5 GSC ATAC-seq

description:
GSC clone
Raw data file: G498_5_SF_AT_3_CAGAGAGG_L008_R1.fastq.gz


title: G498_3 GSC ATAC-seq

description:
GSC clone
Raw data file: G498_3_SF_AT_2_CTCTCTAC_L008_R1.fastq.gz


title: ND240


title: ND241


title: G498_1 GSC ATAC-seq

description:
GSC clone
Raw data file: G498_1_P12_SF_AT_2_TAGGCATG_L005_R1.fastq.gz


title: G498_6 GSC ATAC-seq

description:
GSC clone
Raw data file: G498_6_SF_AT_3_GCTACGCT_L008_R1.fastq.gz


title: ND238


title: ND237


title: G498_2 GSC ATAC-seq

description:
GSC clone
Raw data file: G498_2_SF_AT_2_TAAGGCGA_L008_R1.fastq.gz


title: G800 GSC ATAC-seq

description:
GSC line
Raw data file: G800_P8_SF_AT_1_TAGGCA_L008_R1.fastq.gz


title: G799 GSC ATAC-seq

description:
GSC line
Raw data file: G799.fastq.gz


title: ND236


title: ND239


title: ND235


title: G797 GSC ATAC-seq

description:
GSC line
Raw data file: G797_P9_SF_AT_2_TAGGCATG_L003_R1.fastq.gz


title: G729 GSC ATAC-seq

description:
GSC line
Raw data file: G729.fastq.gz


title: ND234


title: G551_DP3 GSC ATAC-seq

description:
GSC clone
Raw data file: G511_DP3_P13_SF_AT_1_TCCTGA_L008_R1.fastq.gz


title: G744 GSC ATAC-seq

description:
GSC line
Raw data file: G744_P8_SF_AT_1_TAGGCATG_L002_R1.fastq.gz


title: ND233


title: ND230


title: G706 GSC ATAC-seq

description:
GSC line
Raw data file: G706_P8_SF_AT_1_GGACTC_L008_R1.fastq.gz


title: ND229


title: G719 GSC ATAC-seq

description:
GSC line
Raw data file: G719.fastq.gz


title: ND227


title: G705 GSC ATAC-seq

description:
GSC line
Raw data file: G705_P9_SF_AT_1_AGGCAGAA_L003_R1.fastq.gz


title: G702 GSC ATAC-seq

description:
GSC line
Raw data file: G702_P11_SF_AT_1_GGACTCCT_L004_R1.fastq.gz


title: G620 GSC ATAC-seq

description:
GSC line
Raw data file: G620_P8_SF_AT_2_TCCTGAGC_L006_R1.fastq.gz


title: ND226

description:
NGT_all_R1_RPKM_nocap_sg.csv
Vagal_TargetSeq


title: ND228


title: G613 GSC ATAC-seq

description:
GSC line
Raw data file: G613_P12_SF_AT_2_GGACTCCT_L005_R1.fastq.gz


title: ND225


title: ND222


title: G648 GSC ATAC-seq

description:
GSC line
Raw data file: G648_P14_SF_AT_1_AGGCAGAA_L004_R1.fastq.gz


title: G594 GSC ATAC-seq

description:
GSC line
Raw data file: G594_P8_SF_AT_1_AGGCAG_L008_R1.fastq.gz


title: ND221


title: G584 GSC ATAC-seq

description:
GSC line
Raw data file: G584_P8_SF_AT_1_TAGGCATG_L008_R1.fastq.gz


title: G577 GSC ATAC-seq

description:
GSC line
Raw data file: G577_P10_SF_AT_1_GGACTCCT_L002_R1.fastq.gz


title: G583 GSC ATAC-seq

description:
GSC line
Raw data file: G583_P11_SF_AT_3_TCCTGAGC_L005_R1.fastq.gz


title: ND220


title: G571 GSC ATAC-seq

description:
GSC line
Raw data file: G571_P11_SF_AT_1_TAGGCATG_L003_R1.fastq.gz


title: G567 GSC ATAC-seq

description:
GSC line
Raw data file: G567_P8_SF_AT_1_GGACTCCT_L008_R1.fastq.gz


title: G566 GSC ATAC-seq

description:
GSC line
Raw data file: G566.fastq.gz


title: ND218


title: ND219


title: ND217


title: ND216


title: G551 GSC ATAC-seq

description:
GSC line
Raw data file: G551.fastq.gz


title: ND215


title: ND211


title: G498 GSC ATAC-seq

description:
GSC line
Raw data file: G498_P8_SF_AT_1_AGGCAGAA_L002_R1.fastq.gz


title: G523 GSC ATAC-seq

description:
GSC line
Raw data file: G523_P9_SF_AT_2_TCCTGAGC_L005_R1.fastq.gz


title: ND214


title: ND224


title: G564 GSC ATAC-seq

description:
GSC line
Raw data file: G564.fastq.gz


title: G549 GSC ATAC-seq

description:
GSC line
Raw data file: G549_P8_SF_AT_1_AGGCAGAA_L008_R1.fastq.gz


title: ND208


title: ND210


title: G411 GSC ATAC-seq

description:
GSC line
Raw data file: G411.fastq.gz


title: ND205


title: G361 GSC ATAC-seq

description:
GSC line
Raw data file: G361.fastq.gz


title: G489 GSC ATAC-seq

description:
GSC line
Raw data file: G489_P14_SF_AT_1_AGGCAGAA_L003_R1.fastq.gz


title: ND204


title: ND203


title: ND200


title: GHSROS-LNCaP rep 3

description: stranded

data_processing:
Pre-processing of raw FASTQ reads, including elimination of contaminating adapters, was performed with scythe v0.994 (https://github.com/vsbuffalo/scythe)
Mouse reads were filtered from xenograft samples prior to alignment using Xenome v1.0.1 [22689758].
FASTQ files were aligned to the human genome, build hg19 downloaded from the Illumina iGenome resource at http://goo.gl/LspLBZ, using Bowtie2 v2.1.0 [PMID 22388286] and the spliced-read mapper TopHat (v2.0.9) [PMID 23618408] and reference gene annotations to guide the alignment (-G argument in TopHat).
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using a Cufflinks v2.1.1 [PMID 22383036], with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample (abundance measurements).

source_name: LNCaP prostate cancer cell line

growth_protocol: Human PCa cell lines LNCaP (ATCC CRL-1435) were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen, Mulgrave, VIC, Australia) with 10 % New Zealand Cosmic Calf Serum (FCS, Thermo Fisher Scientific Australia, Scoresby, VIC, Australia). All media was supplemented with 100 U/mL penicillin G and 100 ng/mL streptomycin (Invitrogen).

extract_protocol:
At end point, the primary tumour was resected, divided in half; snap frozen and stored at -80°C. Total RNA was extracted from cell pellets using an RNeasy Plus Mini Kit (QIAGEN, Melbourne, Australia) with a genomic DNA (gDNA) Eliminator spin column, according to the manufacturer’s instructions. RNA purity was analysed using the Agilent 2100 Bioanalyzer, and RNA with an RNA integrity number above 7 used for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq stranded mRNA library)

treatment_protocol: LNCaP-GHSROS (over-expressing) and vector control cells were introduced into 3-week old male mice (NOD/SCID) (Jackson Laboratories; supplied by the animal Resource Centre, Western Australia). Cells were subcutaneously injected in a 1:1 ratio with a Matrigel into the hind flank region of the mice.

tag: cell line

value: LNCaP


title: GHSROS-LNCaP rep 4

description: stranded


title: ND201


title: ND202


title: ND198


title: GHSROS-LNCaP rep 1

description: stranded


title: GHSROS-VECTOR  LNCaP rep 3

description: stranded


title: GHSROS-LNCaP rep 2

description: stranded


title: GHSROS-VECTOR  LNCaP rep 1

description: stranded


title: GHSROS-VECTOR  LNCaP rep 2

description: stranded


title: ND197


title: ND196


title: ND199


title: ND195


title: ND194


title: GHSROS-PC3 rep 1

description: strand-specific

data_processing:
Pre-processing of raw FASTQ reads, including elimination of contaminating adapters, was performed with scythe v0.994 (https://github.com/vsbuffalo/scythe)
FASTQ files were aligned to the human genome, build hg19 downloaded from the Illumina iGenome resource at http://goo.gl/LspLBZ, using Bowtie2 v2.1.0 [PMID 22388286] and the spliced-read mapper TopHat (v2.0.9) [PMID 23618408] and reference gene annotations to guide the alignment (-G argument in TopHat).
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using a Cufflinks v2.1.1 [PMID 22383036], with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample (abundance measurements).

source_name: PC3 prostate cancer cell line

growth_protocol: Human PCa cell lines PC3 (ATCC CRL-1435) were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen, Mulgrave, VIC, Australia) with 10 % New Zealand Cosmic Calf Serum (FCS, Thermo Fisher Scientific Australia, Scoresby, VIC, Australia). All media was supplemented with 100 U/mL penicillin G and 100 ng/mL streptomycin (Invitrogen).

extract_protocol:
Total RNA was extracted from cell pellets using an RNeasy Plus Mini Kit (QIAGEN, Melbourne, Australia) with a genomic DNA (gDNA) Eliminator spin column, according to the manufacturer’s instructions. RNA purity was analysed using the Agilent 2100 Bioanalyzer, and RNA with an RNA integrity number above 7 used for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq stranded mRNA library)

treatment_protocol: PC3-GHSROS (over-expressing) and vector control cells were grown in vitro.


title: GHSROS-PC3 rep 3

description: strand-specific


title: GHSROS-VECTOR rep 2

description: strand-specific


title: GHSROS-VECTOR rep 3

description: strand-specific


title: GHSROS-PC3 rep 2

description: strand-specific


title: ND191


title: ND190


title: ND193


title: shsy_cyto

city: Uppsala

first: Asa

middle: Kristina

last: Bjorklund

address: Box 596

department: Cell and Molecular Biology

country: Sweden

institute: Uppsala University

data_processing:
Reads shorter than 36bp were filtered out and adaptor sequences were trimmed from the remaining data using cutadapt v1.9.1.
Read alignment was done with STAR v2.4.2
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression was quantified from the alignments using HTSeq count (v0.6.1) [70] by providing Ensembl gene annotation (v75) in GTF format.

source_name: SHSHY-5 cell line

extract_protocol:
Nuclear and cytosolic fractions were separated using protocol from Zaghlool A, Ameur A, Nyberg L, Halvardson J, Grabherr M, Cavelier L, Feuk L: Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues. BMC Biotechnol 2013, 13:99.
Only cytoplasmic RNA was treated with the Ribo-Zero Magnetic Gold Kit for human/mouse/Rat (Epicentre) to remove ribosomal RNA, and purified using Agencourt RNAClean XP Kit (Beckman Coulter). The rRNA depleted cytoplasmic RNA and nuclear RNA. Sequencing libraries were prepared using the Ion Total RNA-Seq Kit for the AB Library Builder™ System and quantified using the Fragment analyzer (Advance Analytical) were then treated with RNaseIII according to Ion Total RNA-Seq protocol v2 and purified with Magnetic Bead Cleanup Module (Thermo Fisher).

value: SHSHY-5 cell line

tag: fraction

value: cytoplasmic


title: GHSROS-VECTOR rep 1

description: strand-specific


title: shsy_nuc

tag: tissue

value: nuclear


title: ND192


title: ND186


title: ND187


title: fc_adult_nuc_194_9

source_name: frontal cortex (adult)

value: frontal cortex (adult)

tag: Sex

value: female

tag: individual

value: Adult 5


title: ND185


title: ND188


title: ND180


title: fc_adult_nuc_194_7

value: Adult 3


title: ND179


title: ND182


title: fc_adult_nuc_194_6

value: Adult 2


title: fc_adult_nuc_194_11

value: Adult 1


title: ND184


title: fc_adult_nuc_194_8

value: Adult 4


title: fc_adult_cyto194_3


title: ND176


title: fc_adult_cyto194_2


title: fc_adult_cyto194_5

value: Adult 6


title: ND175


title: ND183


title: fc_adult_cyto194_0


title: ND173


title: ND174


title: fc_adult_cyto194_4


title: cer_fetal_nuc64_8

source_name: cerebellum (fetal)

value: cerebellum (fetal)

value: Fetal 3


title: cer_fetal_cyto63_8


title: ND172

value: nodose ganglion


title: ND171

value: post natal 8-12 weeks


title: fc_fetal_nuc64_7

source_name: frontal cortex (fetal)

value: frontal cortex (fetal)


title: fc_fetal_cyto63_7


title: ND168

value: wild type


title: ND169


title: fc_fetal_nuc64_5

value: Fetal 2


title: ND177


title: cer_fetal_cyto63_6

value: cytoplasmic


title: ND167


title: cer_fetal_nuc64_6

value: nuclear


title: fc_adult_nuc_194_10

value: frontal cortex (adult)


title: ND178


title: fc_adult_cyto194_1

value: female


title: ND164


title: ND166


title: ND165


title: fc_fetal_cyto63_5


title: cer_fetal_cyto63_4

value: male

value: Fetal 1


title: cer_fetal_nuc64_4


title: ND162


title: ND163


title: fc_fetal_nuc64_3


title: RNAseq_shCTRL_bio2

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

description: RNA-seq data

data_processing:
Reads were aligned to the human genome (hg19) using STAR (version 2.5.2) with default option
Reads assigned to exons were estimated by the RSEM program (version 1.2.31) and normalized using DESeq2 package (version 3.7).
Genome_build: hg19
Supplementary_files_format_and_content: Normalized score were calculated by DESeq2

source_name: Raji cell

growth_protocol: EBV positive B-cell (Mutu I, LCL, Raji) were grown in RPMI with 10% FBS and Glutamax

extract_protocol:
Total RNA was isolated for RNA-Seq using Trizol reagent.
RNA seq samples was constructed using the QuantSeq 3' mRNA-Seq library prep kit (LEXOGEN) according to manufacturers instructions.

value: Raji cell


title: RNAseq_shCTRL_bio1

description: RNA-seq data


title: ND160


title: ND161


title: ND159


title: RNAseq_shEBNA1_bio1

description: RNA-seq data


title: ND158


title: RNAseq_shEBNA1_bio2

description: RNA-seq data


title: ND154


title: H3K9me3_MutuI

data_processing:
Reads were aligned to the human genome (hg19) using Bowtie2 (version 2.2.9) with default option
Reads aligned to same location were kept only 1 and rest of remaining reads were discarded by Picard (version 2.7.1) because those are likely derived from PCR artifact.
Reads with low mapping quality (MapQ < 10) and from repetitive sequences were discarded.
Pileup score were calculated using Homer software (version 4.10.1)
genome build: hg19
processed data files format and content: Bigwig files were generated using bedGraphToBigWig software.

source_name: MutuI cell

growth_protocol: EBV positive B-cell (Mutu I, LCL, Raji) were grown in RPMI with 10% FBS and Glutamax.

extract_protocol:
The 4C-seq was performed as previously reported with some modifications (van de Werken et al, 2012 Nat Methods 9, 969-972). For each primer view-point from EBV genome, a total 10 to 100 ng DNA was amplified by PCR. ChIP-Seq protocol is as described previously (Lu et al, 2010 Virology journal 7, 262).
4C-Seq Library was amplified with the NEBNext UltraII DNA library prep kit for Illumina (NEB E7645). ChIP-Seq Library was constructed using the TruSeq ChIP Sample Prep kit (Illumina) according to manufacturer's instructions.

value: MutuI cell


title: ND153


title: H3K9me3_Mutu-LCL

source_name: MutuI-LCL cell

value: MutuI-LCL cell


title: CTCF_Mutu-LCL


title: ND151


title: ND155


title: CTCF_MutuI


title: Mutu-LCL (2)_LMP_Csp6I_bio2

data_processing:
Library strategy: 4C-seq
The 75 bp sequence reads were grouped by cutadapt (version 1.11) based on the sequence from 4C bait location. Reads from bait location were truncated.
Reads were aligned to human genome (hg19) using Bowtie2 (version 2.2.9) with iterative alignment strategy.
Reads with low mapping quality (MapQ < 10) and repeat derived reads were removed.
Total aligned reads for non-overlapping 10 kb window were calculated. P-values from a Poisson distribution of reads (except EBV aligned reads) were used for peak calling by MACS2 software (version 2.1.1) with the parameters: ‘-c 5 -l 20000 -g 10000
genome build: hg19
processed data files format and content: Total reads for every 10kb non-overlapped windows were calculated for MutuI and Raji cell. Total reads for every 500kb window with 10kb sliding were calculated for LCL cell. Those reads were converted to bigwig file using bedGraphToBigWig software. Peaks of 10kb windows were converted to bigbed using bedGraphToBigWig software.

tag: bait location

value: LMP

tag: restriction enzyme

tag: replicate


title: Mutu-LCL (2)_LMP_Csp6I_bio1


title: ND152

data_processing:
all samples: HighSeq 4000 were used for sequecing and de-multiplexed to generate a fastq file.
For Sample 1: De-multiplexing alignment to the mm10 transcriptome and unique molecular identifier (UMI)-collapsing were performed using Cell Ranger version 2.0.1, available from 10x Genomics with default parameters.
For all other samples: Reads were aligned to annotated mRNAs in the mouse genome (UCSC, Mus musculus assembly mm10) and the read count for each gene was calculated using ArrayStar software (DNAstar).
Genome_build: mm10
Supplementary_files_format_and_content: mtx file generated by Cell Ranger v2.0.1, including all cells in Sample 1
Supplementary_files_format_and_content: csv file include reads values for all cells (ND1-501) other than sample 1


title: Mutu-LCL (2)_LMP_MboI_bio2

value: MboI


title: ND148


title: ND147


title: ND143


title: Mutu-LCL (2)_Qp_MboI_bio2

value: Qp


title: Mutu-LCL (2)_Qp_Csp6I_bio1


title: fc_fetal_cyto63_3


title: Mutu-LCL (2)_Cp_Csp6I_bio1

value: Cp


title: Mutu-LCL (2)_Cp_MboI_bio2


title: Mutu-LCL (2)_Qp_Csp6I_bio2


title: ND140

value: nodose ganglion

value: post natal 8-12 weeks


title: ND142

value: wild type


title: ND139


title: ND138


title: ND136


title: ND134


title: Mutu-LCL (2)_OriP_Csp6I_bio2

value: OriP


title: ND149


title: Mutu-LCL (2)_FR_Csp6I_bio2

value: FR


title: Mutu-LCL (2)_LMP_MboI_bio1


title: ND146


title: ND157


title: ND131


title: ND137


title: Mutu-LCL (2)_FR_MboI_bio1


title: ND144


title: ND141


title: ND150


title: Mutu-LCL (1)_LMP_Csp6I_bio1


title: Mutu-LCL (2)_Qp_MboI_bio1


title: ND133


title: Mutu-LCL (2)_Cp_MboI_bio1


title: Mutu-LCL (2)_Cp_Csp6I_bio2


title: Mutu-LCL (2)_OriP_Csp6I_bio1


title: Mutu-LCL (1)_Qp_Csp6I_bio2


title: Mutu-LCL (1)_LMP_MboI_bio1


title: ND125


title: Mutu-LCL (2)_OriP_MboI_bio2


title: Mutu-LCL (2)_OriP_MboI_bio1


title: ND121


title: Mutu-LCL (2)_FR_Csp6I_bio1


title: Mutu-LCL (1)_Qp_MboI_bio1


title: Mutu-LCL (1)_Cp_MboI_bio2


title: ND130


title: Mutu-LCL (1)_LMP_Csp6I_bio2


title: ND117


title: Mutu-LCL (1)_OriP_Csp6I_bio2


title: ND129


title: ND128


title: ND116


title: ND127


title: Mutu-LCL (1)_LMP_MboI_bio2


title: Mutu-LCL (2)_FR_MboI_bio2


title: ND126


title: Mutu-LCL (1)_Qp_Csp6I_bio1


title: ND111


title: ND132


title: Mutu-LCL (1)_FR_MboI_bio2


title: ND109


title: Mutu-LCL (1)_Qp_MboI_bio2


title: ND122


title: ND123


title: ND114


title: Mutu-LCL (1)_Cp_Csp6I_bio2


title: Mutu-LCL (1)_FR_Csp6I_bio1


title: Mutu-LCL (1)_Cp_Csp6I_bio1


title: ND120


title: ND124


title: Raji_LMP_MboI_bio2


title: ND119


title: Mutu-LCL (1)_Cp_MboI_bio1


title: Raji_LMP_Csp6I_bio2


title: ND118


title: Mutu-LCL (1)_OriP_Csp6I_bio1


title: ND104


title: ND103


title: ND115


title: Mutu-LCL (1)_OriP_MboI_bio1


title: ND102


title: Mutu-LCL (1)_FR_Csp6I_bio2


title: ND101


title: ND113


title: ND110


title: ND098


title: ND096


title: ND097


title: Mutu-LCL (1)_OriP_MboI_bio2


title: ND107


title: Raji_LMP_MboI_bio1


title: Raji_Qp_MboI_bio2


title: Raji_Cp_Csp6I_bio2


title: Raji_Qp_MboI_bio1


title: ND106


title: ND095


title: Raji_LMP_Csp6I_bio1


title: Mutu-LCL (1)_FR_MboI_bio1


title: Raji_Qp_Csp6I_bio1


title: ND100


title: ND099


title: ND093


title: ND094


title: Raji_OriP_Csp6I_bio2


title: Raji_Qp_Csp6I_bio2


title: Raji_Cp_Csp6I_bio1


title: Raji_OriP_Csp6I_bio1


title: Raji_Cp_MboI_bio2


title: Raji_OriP_MboI_bio1


title: Raji_FR_Csp6I_bio2


title: Raji_FR_Csp6I_bio1


title: ND092


title: ND089


title: MutuI_LMP_Csp6I_bio1


title: Raji_OriP_MboI_bio2


title: Raji_Cp_MboI_bio1


title: ND090


title: MutuI_Qp_Csp6I_bio2


title: Raji_FR_MboI_bio1


title: ND087


title: ND088


title: ND091


title: ND085


title: ND086


title: MutuI_LMP_Csp6I_bio2


title: MutuI_LMP_MboI_bio2


title: ND078


title: MutuI_Qp_MboI_bio1


title: MutuI_Cp_Csp6I_bio2


title: ND082


title: Raji_FR_MboI_bio2


title: MutuI_LMP_MboI_bio1


title: MutuI_Cp_MboI_bio2


title: ND080


title: ND081


title: ND079


title: ND075


title: MutuI_Cp_Csp6I_bio1


title: ND072


title: ND074


title: MutuI_OriP_Csp6I_bio1


title: MutuI_OriP_Csp6I_bio2


title: MutuI_OriP_MboI_bio2


title: ND069


title: MutuI_Qp_Csp6I_bio1


title: ND070


title: ND067


title: ND066


title: MutuI_Qp_MboI_bio2


title: MutuI_FR_Csp6I_bio2


title: MutuI_OriP_MboI_bio1


title: ND077


title: MutuI_FR_Csp6I_bio1


title: ND065


title: ND064


title: MutuI_Cp_MboI_bio1


title: ND071


title: Esm1+ ECs Rep3

description:
bone marrow Tomato+/GFP+ cells
All_FPKM.txt

source_name: Femur/Tibia

extract_protocol:
Adult mouse bone samples were crashed with pestle, treated with collagenase IV, and digested to single cells. These single cell suspension were stained for FACS sorting. FACS sorted cell population were directly lysis into RLT buffer and RNA were extracted using RNeasy plus Micro Kit (Qiagen)
Double strand cDNA was synthesized using SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara) and sequencing library was constructed with Nextera XT DNA Library preparation kit (illumina).

value: 8-12 weeks

value: Tamoxifen

value: Esm1-CreER R26-mTmG


title: ND073

extract_protocol:
Nodose ganglion cells are dissociated using a combination of papain/collagenase/dispase solution. 10x Genomics (Sample 1) or Smart-Seq 2 (all other samples) was used to prepare cDNA library
Sequencing library is prepared follow the instruction of 10x Genomics (Sample 1) or using Nextera DNA Library Prep Kit (all other samples)


title: 9Gy1D ECs Rep2

value: 9 Gy irradiation


title: MutuI_FR_MboI_bio1


title: ND063


title: ND062


title: Control

city: Harbin

first: Ning

last: Gu

address: No. 92 West Da-zhi Street

country: China

institute: School of Life Science and Technology, Harbin Institute of Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.1.0 with default parameters
Transcript assembly and FPKM (RPKM) estimated for RNA-Seq data using Cufflinks v2.2.1.0 with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After ultrasonic wave stirring for 30 min, TiO2 NP suspensions (50 mg/kg b.w. per day) were given to NP group mice by oral administration with a syringe. Control group mice were given an equal volume of PBS.

value: liver

value: treated with PBS


title: 9Gy1D ECs Rep1

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
Tophat (v2.1.1) used for alignment
HTSeq-count (v0.6.1) used for transcriptome abundance measurement
DESeq2(v1.18.1) used for differential gene expression analyses
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample


title: ND061


title: ND060


title: ND056


title: 9Gy1D ECs Rep3


title: Diaphysis EC Rep3

description:
Diaphysis GFP+ cells
Apln_DP_fpkms.txt
DP_EC-3

source_name: Femur

extract_protocol:
Adult mouse bone samples were crashed with pestle, treated with collagenase IV, and digested to single cells. These single cell suspension were stained for FACS sorting. FACS sorted cell population were directly lysis into RLT buffer and RNA were extracted using RNeasy plus Micro Kit (Qiagen)
Double strand cDNA was synthesized using SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara) and sequencing library was constructed with Nextera XT DNA Library preparation kit (illumina). TruSeq Stranded Total RNA kit (Illumina) was used for the library preparation of total BMC and Lin- samples.


title: NP

value: treated with TiO2 NPs


title: ND057


title: ND059


title: MutuI_FR_MboI_bio2

value: MutuI cell


title: Esm1+ ECs Rep2


title: Esm1+ ECs Rep1


title: ND055


title: ND054


title: KOV1: Long-term survivor (HG-U133A)

city: Brescia

first: Antonella

last: Ravaggi

state: Brescia

address: Viale Europa 11

department: Department of Clinical and Experimental Sciences

country: Italy

institute: University of Brescia

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 °C on GeneChip® Human Genome U133A oligonucleotide microarray chips (Affymetrix, Inc., Santa Clara, CA, USA) following the manufacturer’s protocols. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner  3000 7G.

data_processing: The data were analyzed with Affymetrix Gene Chip Command Console Software, using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: ovarian cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

extract_protocol: Total RNA was extracted and purified from snap-frozen biopsies containing at least 70% of tumor epithelial cells by TRIzolⓇ Reagent (ThermoFisher) according to manufacturer’s instructions.

value: ovary

tag: tumor stage

value: IIIC

tag: tumor histotype

value: high grade serous

tag: phenotype

value: platinum sensitive


title: KOV2: Long-term survivor (HG-U133A)


title: Apln+ EC Rep3

description:
whole bone GFP+ cells
Apln_DP_fpkms.txt
Apln_EC-3

tag: treatment

value: tamoxifen

value: Apln-CreERT2 R26-mTmG


title: Diaphysis EC Rep2

description:
Diaphysis GFP+ cells
Apln_DP_fpkms.txt
DP_EC-2


title: KOV3: Long-term survivor (HG-U133A)

value: platinum partially sensitive


title: Diaphysis EC Rep1

description:
Diaphysis GFP+ cells
Apln_DP_fpkms.txt
DP_EC-1


title: ND053

description:
NGT_all_R1_RPKM_nocap_sg.csv
Vagal_TargetSeq

value: nodose ganglion

value: post natal 8-12 weeks

value: wild type


title: ND052


title: KOV5: Long-term survivor (HG-U133A)

value: IV


title: ND050